def _createStat(self, *args, **kwArgs):
assert(isinstance(args[0], TrackView))
tv1 = args[0]
if len(args) > 1 and isinstance(args[1], TrackView):
tv2 = args[1]
assert(tv1.genomeAnchor == tv2.genomeAnchor)
#Temporary hack for multiple tracks
# if len(args) > 2:
extraTrackViews = [arg for arg in args[2:] if isinstance(arg, TrackView)]
self.stat = self.CLASS_TO_CREATE(kwArgs['binRegs'] if 'binRegs' in kwArgs else tv1.genomeAnchor, \
SampleTrack(tv1) if kwArgs.get('testWithConverter') != True else SampleTrackWithConverters(tv1),\
SampleTrack(tv2) if kwArgs.get('testWithConverter') != True else SampleTrackWithConverters(tv2),\
*args[2 + len(extraTrackViews):], **kwArgs)
#Temporary hack for multiple tracks
for tv in extraTrackViews:
track = SampleTrack(tv) if kwArgs.get('testWithConverter') != True else SampleTrackWithConverters(tv)
if hasattr(self.stat, '_tracks'):
self.stat._tracks.append(track)
else:#for splittable
if 'extraTracks' not in self.stat._kwArgs:
self.stat._kwArgs['extraTracks'] = tuple()
self.stat._kwArgs['extraTracks'] += tuple([track])
else:
self.stat = self.CLASS_TO_CREATE(kwArgs['binRegs'] if 'binRegs' in kwArgs else tv1.genomeAnchor, \
SampleTrack(tv1) if kwArgs.get('testWithConverter') != True else SampleTrackWithConverters(tv1),\
*args[1:], **kwArgs)
def _getSampleTrack(numbers=False):
if numbers:
return SampleTrack(SampleTV_Num(anchor=[0, 50]), True)
else:
return SampleTrack(
SampleTV(starts=True,
ends=True,
vals=True,
numElements=50,
anchor=[0, 1000]), True)
def _doRandTest(self, origTV, randTrackClasses):
anchor = [origTV.genomeAnchor.start, origTV.genomeAnchor.end]
intensityTV = SampleTV_Num(vals=range(anchor[1] - anchor[0]),
anchor=anchor) # fixme: not yet used..
MyPlainTrack._origTV = intensityTV
gold.track.SegsSampledByIntensityTrack.PlainTrack = MyPlainTrack
origTrack = SampleTrack(origTV)
anchorReg = GenomeRegion('TestGenome', 'chr21', anchor[0], anchor[1])
binLen = len(anchorReg)
for randClass in randTrackClasses:
for i in range(100):
randTrack = randClass(origTrack,
i,
trackNameIntensity='dummy_intensity')
randTV = randTrack.getTrackView(anchorReg)
self.assertListsOrDicts(sorted(len(el) for el in origTV),
sorted(len(el) for el in randTV))
if isinstance(randClass, PermutedSegsAndIntersegsTrack):
self.assertEqual(self._getInterSegLens(origTV, binLen),
self._getInterSegLens(randTV, binLen))
else:
self.assertEqual(
sum(self._getInterSegLens(origTV, binLen)),
sum(self._getInterSegLens(randTV, binLen)))
for el in randTV:
assert (0 <= el.start() < el.end() <= binLen)
# self.assertEqual(self._createValAndStrandDict(origTV), self._createValAndStrandDict(randTV))
self.assertListsOrDicts(self._createSortedContents(origTV),
self._createSortedContents(randTV))
def _doRandTest(self, origTV):
origTrack = SampleTrack(origTV)
queryReg = GenomeRegion('TestGenome','chr21',100,400)
for randClass in [RandomGenomeLocationTrack]:
for i in range(10):
randTrack = randClass(origTrack, i)
randTV = randTrack.getTrackView(queryReg)
self.assertEqual(len(queryReg), len(randTV))
def setUp(self):
"""
Create a fake trackstructure containing empty tracks,
this is only used to ensure the randomization pool knows there should be 3 input tracks.
"""
genomeAnchor = [0, 101]
self.amountTracks = 3
self.region = GenomeRegion('TestGenome', 'chr21', genomeAnchor[0],
genomeAnchor[1])
self.ts = TrackStructureV2()
for i, segmentSet in enumerate([[]] * self.amountTracks):
track = SampleTrack(
SampleTV(segments=segmentSet, anchor=genomeAnchor))
track.getUniqueKey = MagicMock(return_value=i)
self.ts[str(i)] = SingleTrackTS(track, {})
self.shufflePool = ShuffleElementsBetweenTracksPool(
self.ts, self.region, None)
def setUp(self):
genomeAnchor = [0, 101]
self.bins = [
GenomeRegion('TestGenome', 'chr21', 0, 50),
GenomeRegion('TestGenome', 'chr21', 50, 101)
]
self.ts = defaultdict(TrackStructureV2)
allSegmentSetNoOverlap = [[[10, 20]],
[[5, 10], [25, 50], [55, 70], [75, 80],
[90, 95]],
[[5, 15], [20, 30], [45, 55], [75, 80]],
[[0, 20], [60, 65], [85, 100]]]
allSegmentSetOverlap = [[[10, 25]],
[[5, 10], [20, 50], [55, 70], [75, 80],
[90, 95]],
[[5, 20], [15, 30], [45, 55], [75, 80]],
[[0, 20], [60, 65], [85, 100]]]
excludedSegments = [[45, 55], [70, 75]]
for allowOverlaps, allSegmentSet in \
zip([False, True], [allSegmentSetNoOverlap, allSegmentSetOverlap]):
for i, segmentSet in enumerate(allSegmentSet):
track = SampleTrack(
SampleTV(segments=segmentSet,
anchor=genomeAnchor,
allowOverlaps=allowOverlaps))
track.getUniqueKey = MagicMock(return_value=i)
self.ts[allowOverlaps]['dummy' + str(i)] = SingleTrackTS(
track, {})
track = SampleTrack(
SampleTV(segments=[],
anchor=genomeAnchor,
allowOverlaps=allowOverlaps))
track.getUniqueKey = MagicMock(return_value=i + 1)
self.ts[allowOverlaps]['emptyTrack'] = SingleTrackTS(track, {})
exclusionTrack = SampleTrack(
SampleTV(segments=excludedSegments,
anchor=genomeAnchor,
allowOverlaps=False))
self.exclusionTs = SingleTrackTS(exclusionTrack, {})
def provideTrack(tn):
valList = tn[0].split(',')
return SampleTrack(SampleTV_Num( vals=valList, anchor=[0,len(valList)] ))